Annotation of PDB with respect to \DisorderedRegions" in Proteins
Meeta Rani

1meeta@bic.nus.edu.sg
123

Pedro Romero

2

Zoran Obradovic

promero@eecs.wsu.edu

2zoran@eecs.wsu.edu

A. Keith Dunker

3dunker@mail.wsu.edu

BioInformatics Centre, National University of Singapore, 10 Kent Ridge Crescent,Singapore 11926099
Department of Electrical Engineering and Computer Science, Washington State University, Pullman, WA, 99164, USA
Department of Biochemistry and Biophysics, Washington State University, Pullman,WA, 99164, USA

1 Introduction
Protein function has conventionally been associated with three-dimensional structure, with the understanding that folding is a prerequisite to function. On the contrary, there exist proteins containing
regions that do not fold as expected but are required for important biological functions. We call these\disordered" regions.
Disorder provides the basis for numerous functions, but an especially interesting one is the involvement of disorder in molecular recognition. This appears contrary to the long-held views ofcomplementary surface tting for binding, but such disordered regions typically become ordered as
the proteins associate with their cognate molecules thereby leading to surface complementarity in thecomplex. Well-characterized examples include enzyme-substrate, receptor-ligand, protein-peptide,protein-protein, protein-RNA and protein-DNA complexes. It has been suggested that disorder-ordertransitions allow biologically advantageous combination of high speci city coupled with low anity.
If disordered regions are so involved in function then they are likely to have distinctive amino acidsequences.
Disordered regions in proteins can be random coil-like, molten globule-like or somewhere in between. Such regions can be identi ed by hypersensitivity to protease digestion, absence of coordinatesin the x-ray data and characterization by CD or NMR spectroscopy. Using these methods, hundredsof examples of disordered regions are now known.
We have initiated work on the sequence-disorder relationships [1]. The single greatest dicultyin our studies is the lack of organized information on disordered regions. For example, although
the Protein Data Bank probably contains the largest collection of information regarding disordered
proteins, this information is very dicult to retrieve as the disordered regions are not reported orannotated in any uniform way [2]. Even worse is that disordered regions are sometimes obscured by
the use of model building to add the missing coordinates.
Given the growing realization of the importance of disordered regions, we feel it is very timely
and useful to annotate and classify the proteins in the PDB with speci c reference to disorder. Since
disordered regions are unobservable in the x-ray data, this property can be used as a criterion formarking a PDB entry as containing a disordered region and then for further classi cation based on
this information. However missing coordinates in an X-ray determined structure could arise frommultiple causes, not all of which imply exible disorder (eg., random coil-like or molten globule-likestructures). Therefore annotation of theproteins of the PDB to include information on disorder should
be regarded as a rst step to which information from other sources can be added eventually.
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2 Identi cation and analysis of disordered regions in the PDB
Our study involves three steps: identi cation, annotation and classi cation of the disordered regionsin the PDB. These 3 steps are described brie y as follows:
A: Identi cation of disordered regions
The coordinates of the atoms are usually not reported in the PDB les. Thus such PDB entries
show fewer amino acids than contained in the actual sequence. To nd all the disordered regionsin the PDB, the number of amino acids in the structure les are compared with the actual numberof amino acids in them. All proteins for which there are discrepancies in these two data are saved.
Next, the amino acids in the co-ordinate list are compared one-by-one to amino acids in the sequence.
Sequence discrepancies are agged for manual investigation and amino acids that are missing fromthe coordinate lists are identi ed to constitute disordered regions in the proteins.
B: Annotation of the disordered regions
A new keyword, say, DS (short for \disorder status") will be added to each entry and the following
information will be inserted in each record. DS: (disorder status): a disordered region is PRESENTor ABSENT. If DS = PRESENT then a) Position of DR in the protein: position x to position y.
b) Vicinity of DR: C-terminus/N-terminus/ internal to sequence c) Class: based on length of DR(see below). d) Percentage of amino acids in DR: x% of length. e) Function: con rmed or putativedescription of the function. f) Comments: Important information regarding further characterizationof the given DR, by NMR or such as hypersensitivity to protease action may be added.
C: Classi cation of the disordered regions
Our initial classi cation of the disordered regions will be based on their lengths. The rationaleis that di erent lengths of disordered regions will have di erent potential capabilities. Our tentative
grouping will be: a) Very short disordered regions, 1-8 AA. b) Short disordered regions, 9-19 AA. c)
Medium disordered regions, 20-39 AA. d) Long disordered regions 40-59 AA e) Very long disorderedregions  60 AA.
The annotation and the length-based classi cation of the disordered regions will be included in therecords of the PDB entries and the new database will be called Pdb disorder Plus. This annotateddatabase will provide an organized collection of information on disordered regions in proteins and is
expected to encourage further investigation of disordered regions and their putative functions. On completion, (soon expected to be), Pdb disorder Plus will be jointly shared and maintained by the BioInformatics Centre, National Univ. of Singapore at their home-page (http://www.bic.nus.edu.sg/),and
Department of Biochemistry and Biophysics, WSU, Pullman, USA, at their \Protein Disorder homepage" (http://www.disorder.chem.wsu.edu/).

References[1] Romero P., Obradovic Z., Kissinger C., Villafranca J. E., and Dunker A. K., Identifying Disordered Regions in Proteins from Amino Acid Sequences, Proceedings of the International Conference on Neural Networks (ICNN'97), at Houston, Texas, USA, 90{95, 1997.
[2] Dunker, A.K., Obradovic, Z., Romero, P., Kissinger, C., and Villafranca,J. E., On the Importanceof Being Disordered, PDB Newsletter, 81:3{5, 1997.

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